No problem Changrong, glad to be of help to a fellow scientist. And thanks
to John and the other for showing much more elegant ways of solving the
problem.
Cheers!
Anjan
On Thu, Dec 2, 2010 at 3:40 AM, John W. Krahn <jwkr...@shaw.ca> wrote:
> Changrong Ge wrote:
>
>> Hi guys,
>>
>
> Hello,
>
>
> Thanks a lot for this issue and with Anjan's help here I got the
>> wonderful script for my work and I post below, hopefully it would be
>> helpful
>> for others--works perfectly for fasta file.
>> Also thanks to others who are interested in the discussion, but I
>> think
>> it takes time for me to digest those "weird" symbols-----Tack Så Mycket!!!
>> Have a nice day
>> Changrong
>>
>>
>>
>> usage: perl seqComp.pl<input_fasta_file> > <output_file>
>>
>>
>> #! /usr/bin/perl -w
>> use strict;
>>
>> open (S, "$ARGV[0]") || die "cannot open FASTA file to read: $!";
>>
>> my %s;# a hash of arrays, to hold each line of sequence
>> my %seq; #a hash to hold the AA sequences.
>> my $key;
>>
>> while (<S>){ #Read the FASTA file.
>> chomp;
>>
>> if (/>/){
>> s/>//;
>> $key= $_;
>> }else{
>> push (@{$s{$key}}, $_);
>> }
>>
>> }
>>
>> foreach my $a (keys %s){
>> my $s= join("", @{$s{$a}});
>> $seq{$a}=$s;
>> #print("$a\t$s\n");
>> }
>>
>
> You don't need two loops for that, you could just do:
>
>
> while ( <S> ) { #Read the FASTA file.
> chomp;
>
> if ( s/>// ) {
> $key = $_;
> }
> else {
> $seq{ $key } .= $_;
>
> }
> }
>
>
>
>
> John
> --
> Any intelligent fool can make things bigger and
> more complex... It takes a touch of genius -
> and a lot of courage to move in the opposite
> direction. -- Albert Einstein
>
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>
>
>
--
===================================
anjan purkayastha, phd.
research associate
fas center for systems biology,
harvard university
52 oxford street
cambridge ma 02138
phone-703.740.6939
===================================
